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Doing some development on `workflows` and using sprocket. It's annoying when I run `sprocket lint .wdl` and am faced with a huge number of printed diagnostics from files imported by my workflow. In th…
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From the short reads workflow wdl shortReads_assembly.wdl we need outasmstats, this has the assembly stats, that file needs get propagated to be part of the output of jgi_metaAssembly in jgi_assembly.…
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Hi,
I saw the HiFi somatic workflow https://github.com/PacificBiosciences/HiFi-somatic-WDL/blob/main/figures/simple_workflow_diagram.png. After calling somatic SNV/INDEL(using deepsomatic, tumor/no…
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Hello,
I am trying to run the SHARE-Seq pipeline starting from the preprocessing step on an HPC.
- Could someone share an example JSON and other required preprocessing files for starting the ana…
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This cannot be finished until CoreMS 3.0 is released
Drafting subtasks
- [ ] Write metaMS.lcmsLipidomicsWorkflow module
- [x] Update metaMS.cli module to source metaMS.lcmsLipidomicsWorkflow mo…
kheal updated
1 month ago
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Feedback on the new PROOF UI: Submit a Workflow
It is a bit unintuitive/confusing to have the WDL and JSON in separate boxes.
It would be more “easy” to have them all in the same box and then the lab…
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NMDC has a FY24 Q2 milestone of 'Assembly support for long-read sequence data'. JGI has an existing workflow in WDL which NMDC will adopt.
https://code.jgi.doe.gov/BFoster/jgi_meta_wdl/-/blob/mast…
aclum updated
2 weeks ago
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In several cases in the workflow repository we are not outputting the stats file needed in order for the nmdc_automation code populate mongo records with workflow specific fields (ie contig_bp for nmd…
aclum updated
3 weeks ago
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"project" is input to the workflow to distinguish which dataset the samples belong to.
recommend:
- [ ] change project -> team as argument as the project currently is encoded as "team-"
- [ ]…
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### Feature Request
We are reaching our CPU limit for our production Terra workspace. This is negatively impacting our pipeline and preventing us from reliably meeting dashboard updates.
This is…